[{"acknowledged_ssus":[{"_id":"Bio"}],"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","intvolume":"        11","title":"Cell-surface receptors enable perception of extracellular cytokinins","article_number":"4284","status":"public","oa":1,"author":[{"first_name":"Ioanna","last_name":"Antoniadi","full_name":"Antoniadi, Ioanna"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","last_name":"Plíhal","full_name":"Plíhal, Ondřej"},{"full_name":"Simerský, Radim","last_name":"Simerský","first_name":"Radim"},{"full_name":"Mik, Václav","first_name":"Václav","last_name":"Mik"},{"full_name":"Vain, Thomas","first_name":"Thomas","last_name":"Vain"},{"full_name":"Mateo-Bonmatí, Eduardo","last_name":"Mateo-Bonmatí","first_name":"Eduardo"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"last_name":"Plačková","first_name":"Lenka","full_name":"Plačková, Lenka"},{"first_name":"Korawit","last_name":"Opassathian","full_name":"Opassathian, Korawit"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Doležal","first_name":"Karel","full_name":"Doležal, Karel"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"full_name":"Turnbull, Colin","first_name":"Colin","last_name":"Turnbull"}],"day":"27","citation":{"mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” <i>Nature Communications</i>, vol. 11, 4284, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>.","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>","ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>.","ieee":"I. Antoniadi <i>et al.</i>, “Cell-surface receptors enable perception of extracellular cytokinins,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>","short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020)."},"file":[{"checksum":"5b96f39b598de7510cfefefb819b9a6d","date_updated":"2020-12-10T12:23:56Z","success":1,"file_name":"2020_NatureComm_Antoniadi.pdf","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"8936","file_size":3526415,"date_created":"2020-12-10T12:23:56Z"}],"date_updated":"2023-08-22T09:10:32Z","has_accepted_license":"1","article_type":"original","volume":11,"date_published":"2020-08-27T00:00:00Z","date_created":"2020-09-06T22:01:13Z","month":"08","_id":"8337","language":[{"iso":"eng"}],"ddc":["580"],"publication_status":"published","project":[{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000567931000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses."}],"ec_funded":1,"file_date_updated":"2020-12-10T12:23:56Z","publication_identifier":{"eissn":["20411723"]},"acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","article_processing_charge":"No","type":"journal_article","isi":1,"year":"2020","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-020-17700-9","oa_version":"Published Version"},{"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/337"}],"quality_controlled":"1","page":"623-651","publisher":"Springer Nature","publication":"23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography","intvolume":"     12110","title":"Improved discrete Gaussian and subgaussian analysis for lattice cryptography","status":"public","oa":1,"author":[{"last_name":"Genise","first_name":"Nicholas","full_name":"Genise, Nicholas"},{"first_name":"Daniele","last_name":"Micciancio","full_name":"Micciancio, Daniele"},{"last_name":"Peikert","first_name":"Chris","full_name":"Peikert, Chris"},{"full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Walter","orcid":"0000-0003-3186-2482"}],"conference":{"name":"PKC: Public-Key Cryptography","end_date":"2020-05-07","location":"Edinburgh, United Kingdom","start_date":"2020-05-04"},"day":"15","citation":{"short":"N. Genise, D. Micciancio, C. Peikert, M. Walter, in:, 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography, Springer Nature, 2020, pp. 623–651.","apa":"Genise, N., Micciancio, D., Peikert, C., &#38; Walter, M. (2020). Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i> (Vol. 12110, pp. 623–651). Edinburgh, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">https://doi.org/10.1007/978-3-030-45374-9_21</a>","ieee":"N. Genise, D. Micciancio, C. Peikert, and M. Walter, “Improved discrete Gaussian and subgaussian analysis for lattice cryptography,” in <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, Edinburgh, United Kingdom, 2020, vol. 12110, pp. 623–651.","chicago":"Genise, Nicholas, Daniele Micciancio, Chris Peikert, and Michael Walter. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” In <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, 12110:623–51. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">https://doi.org/10.1007/978-3-030-45374-9_21</a>.","ista":"Genise N, Micciancio D, Peikert C, Walter M. 2020. Improved discrete Gaussian and subgaussian analysis for lattice cryptography. 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography, LNCS, vol. 12110, 623–651.","ama":"Genise N, Micciancio D, Peikert C, Walter M. Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In: <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>. Vol 12110. Springer Nature; 2020:623-651. doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">10.1007/978-3-030-45374-9_21</a>","mla":"Genise, Nicholas, et al. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, vol. 12110, Springer Nature, 2020, pp. 623–51, doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">10.1007/978-3-030-45374-9_21</a>."},"date_updated":"2023-02-23T13:31:06Z","volume":12110,"date_published":"2020-05-15T00:00:00Z","date_created":"2020-09-06T22:01:13Z","month":"05","_id":"8339","language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"Discrete Gaussian distributions over lattices are central to lattice-based cryptography, and to the computational and mathematical aspects of lattices more broadly. The literature contains a wealth of useful theorems about the behavior of discrete Gaussians under convolutions and related operations. Yet despite their structural similarities, most of these theorems are formally incomparable, and their proofs tend to be monolithic and written nearly “from scratch,” making them unnecessarily hard to verify, understand, and extend.\r\nIn this work we present a modular framework for analyzing linear operations on discrete Gaussian distributions. The framework abstracts away the particulars of Gaussians, and usually reduces proofs to the choice of appropriate linear transformations and elementary linear algebra. To showcase the approach, we establish several general properties of discrete Gaussians, and show how to obtain all prior convolution theorems (along with some new ones) as straightforward corollaries. As another application, we describe a self-reduction for Learning With Errors (LWE) that uses a fixed number of samples to generate an unlimited number of additional ones (having somewhat larger error). The distinguishing features of our reduction are its simple analysis in our framework, and its exclusive use of discrete Gaussians without any loss in parameters relative to a prior mixed discrete-and-continuous approach.\r\nAs a contribution of independent interest, for subgaussian random matrices we prove a singular value concentration bound with explicitly stated constants, and we give tighter heuristics for specific distributions that are commonly used for generating lattice trapdoors. These bounds yield improvements in the concrete bit-security estimates for trapdoor lattice cryptosystems."}],"ec_funded":1,"publication_identifier":{"eissn":["16113349"],"isbn":["9783030453732"],"issn":["03029743"]},"article_processing_charge":"No","alternative_title":["LNCS"],"year":"2020","type":"conference","scopus_import":"1","doi":"10.1007/978-3-030-45374-9_21","oa_version":"Preprint"},{"doi":"10.15479/AT:ISTA:8340","supervisor":[{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","year":"2020","type":"dissertation","ec_funded":1,"abstract":[{"text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","file_date_updated":"2021-09-11T22:30:04Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-008-4"]},"language":[{"iso":"eng"}],"_id":"8340","ddc":["572"],"publication_status":"published","department":[{"_id":"LeSa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"degree_awarded":"PhD","has_accepted_license":"1","month":"09","date_published":"2020-09-09T00:00:00Z","date_created":"2020-09-07T18:42:23Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6848"}]},"date_updated":"2023-09-07T13:26:17Z","citation":{"ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","mla":"Kampjut, Domen. <i>Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>.","chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>.","apa":"Kampjut, D. (2020). <i>Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020."},"day":"09","file":[{"checksum":"dd270baf82121eb4472ad19d77bf227c","file_name":"ThesisFull20200908.docx","date_updated":"2021-09-11T22:30:04Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2020-09-08T13:32:06Z","file_size":166146359,"creator":"dkampjut","file_id":"8345","relation":"source_file"},{"embargo":"2021-09-10","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","file_name":"2020_Thesis_Kampjut.pdf","date_updated":"2021-09-11T22:30:04Z","access_level":"open_access","content_type":"application/pdf","date_created":"2020-09-14T15:02:20Z","file_id":"8393","creator":"dernst","relation":"main_file","file_size":13873769}],"status":"public","title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","author":[{"last_name":"Kampjut","first_name":"Domen","full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"page":"242","publisher":"Institute of Science and Technology Austria"},{"month":"09","date_created":"2020-09-08T08:53:53Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2020-09-08T00:00:00Z","degree_awarded":"PhD","has_accepted_license":"1","date_updated":"2023-09-07T13:17:06Z","day":"08","citation":{"short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","apa":"Bezeljak, U. (2020). <i>In vitro reconstitution of a Rab activation switch</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","mla":"Bezeljak, Urban. <i>In Vitro Reconstitution of a Rab Activation Switch</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>."},"file":[{"content_type":"application/x-zip-compressed","access_level":"closed","file_id":"8342","creator":"dernst","relation":"source_file","file_size":65246782,"date_created":"2020-09-08T09:00:29Z","checksum":"70871b335a595252a66c6bbf0824fb02","date_updated":"2021-09-16T12:49:12Z","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip"},{"date_created":"2020-09-08T09:00:27Z","file_size":31259058,"creator":"dernst","file_id":"8343","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_Urban_Bezeljak_Thesis.pdf","date_updated":"2021-09-16T12:49:12Z","checksum":"59a62275088b00b7241e6ff4136434c7"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7580"}]},"author":[{"id":"2A58201A-F248-11E8-B48F-1D18A9856A87","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","last_name":"Bezeljak","first_name":"Urban"}],"oa":1,"status":"public","title":"In vitro reconstitution of a Rab activation switch","page":"215","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:8341","supervisor":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"year":"2020","type":"dissertation","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","file_date_updated":"2021-09-16T12:49:12Z","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MaLo"}],"language":[{"iso":"eng"}],"_id":"8341","ddc":["570"],"publication_status":"published"},{"date_published":"2020-09-09T00:00:00Z","date_created":"2020-09-09T11:12:10Z","month":"09","has_accepted_license":"1","degree_awarded":"PhD","day":"09","citation":{"chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>.","mla":"Shamipour, Shayan. <i>Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes </i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","apa":"Shamipour, S. (2020). <i>Bulk actin dynamics drive phase segregation in zebrafish oocytes </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>"},"file":[{"date_updated":"2021-09-11T22:30:05Z","file_name":"Shayan-Thesis-Final.docx","checksum":"6e47871c74f85008b9876112eb3fcfa1","file_size":65194814,"file_id":"8351","creator":"sshamip","relation":"source_file","embargo_to":"open_access","date_created":"2020-09-09T11:06:27Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"embargo":"2021-09-10","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","file_name":"Shayan-Thesis-Final.pdf","date_updated":"2021-09-11T22:30:05Z","access_level":"open_access","content_type":"application/pdf","date_created":"2020-09-09T11:06:13Z","relation":"main_file","creator":"sshamip","file_id":"8352","file_size":23729605}],"date_updated":"2023-09-27T14:16:45Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"661"},{"id":"6508","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7001","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"735","status":"public"}]},"oa":1,"author":[{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"}],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","status":"public","page":"107","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"None","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"doi":"10.15479/AT:ISTA:8350","year":"2020","type":"dissertation","file_date_updated":"2021-09-11T22:30:05Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."}],"department":[{"_id":"BjHo"},{"_id":"CaHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"_id":"8350","publication_status":"published","ddc":["570"]},{"page":"191","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"oa":1,"author":[{"orcid":"0000-0003-0493-3775","last_name":"Steiner","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","full_name":"Steiner, Julia"}],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","status":"public","citation":{"chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>.","mla":"Steiner, Julia. <i>Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","apa":"Steiner, J. (2020). <i>Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>"},"day":"09","file":[{"file_name":"Thesis_Julia_Steiner_pdfA.pdf","date_updated":"2021-09-16T12:40:56Z","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_created":"2020-09-09T14:22:35Z","creator":"jsteiner","file_id":"8354","relation":"main_file","file_size":117547589,"access_level":"open_access","content_type":"application/pdf"},{"checksum":"ba112f957b7145462d0ab79044873ee9","date_updated":"2020-09-15T08:48:37Z","file_name":"Thesis_Julia_Steiner.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"8355","creator":"jsteiner","file_size":223328668,"date_created":"2020-09-09T14:23:25Z"}],"date_updated":"2023-09-07T13:14:09Z","related_material":{"record":[{"id":"8284","relation":"part_of_dissertation","status":"public"}]},"date_created":"2020-09-09T14:27:01Z","date_published":"2020-09-09T00:00:00Z","month":"09","has_accepted_license":"1","degree_awarded":"PhD","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"department":[{"_id":"LeSa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"_id":"8353","publication_status":"published","ddc":["572"],"file_date_updated":"2021-09-16T12:40:56Z","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner."}],"type":"dissertation","year":"2020","oa_version":"None","supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"doi":"10.15479/AT:ISTA:8353"},{"related_material":{"record":[{"id":"7572","relation":"dissertation_contains","status":"public"},{"status":"public","id":"7197","relation":"part_of_dissertation"}]},"day":"10","citation":{"ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","apa":"Dos Santos Caldas, P. R. (2020). <i>Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8358\">https://doi.org/10.15479/AT:ISTA:8358</a>","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8358\">https://doi.org/10.15479/AT:ISTA:8358</a>.","mla":"Dos Santos Caldas, Paulo R. <i>Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8358\">10.15479/AT:ISTA:8358</a>.","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8358\">10.15479/AT:ISTA:8358</a>"},"file":[{"checksum":"882f93fe9c351962120e2669b84bf088","date_updated":"2020-09-10T12:11:29Z","success":1,"file_name":"phd_thesis_pcaldas.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"pcaldas","file_id":"8364","file_size":141602462,"date_created":"2020-09-10T12:11:29Z"},{"date_updated":"2020-09-11T07:48:10Z","file_name":"phd_thesis_latex_pcaldas.zip","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_size":450437458,"file_id":"8365","relation":"source_file","creator":"pcaldas","date_created":"2020-09-10T12:18:17Z","content_type":"application/x-zip-compressed","access_level":"closed"}],"date_updated":"2023-09-07T13:18:51Z","has_accepted_license":"1","degree_awarded":"PhD","date_published":"2020-09-10T00:00:00Z","date_created":"2020-09-10T09:26:49Z","month":"09","acknowledged_ssus":[{"_id":"Bio"}],"page":"135","publisher":"Institute of Science and Technology Austria","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","status":"public","oa":1,"author":[{"first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","year":"2020","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/AT:ISTA:8358","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"8358","ddc":["572"],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MaLo"}],"abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n","lang":"eng"}],"file_date_updated":"2020-09-11T07:48:10Z","publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","article_processing_charge":"No","alternative_title":["ISTA Thesis"]},{"oa":1,"author":[{"last_name":"Varzi","orcid":"0000-0001-5069-0589","first_name":"Alberto","full_name":"Varzi, Alberto"},{"first_name":"Katharina","last_name":"Thanner","orcid":"0000-0001-5394-2323","full_name":"Thanner, Katharina"},{"first_name":"Roberto","last_name":"Scipioni","orcid":"0000-0003-1926-421X","full_name":"Scipioni, Roberto"},{"last_name":"Di Lecce","first_name":"Daniele","full_name":"Di Lecce, Daniele"},{"last_name":"Hassoun","first_name":"Jusef","full_name":"Hassoun, Jusef"},{"full_name":"Dörfler, Susanne","first_name":"Susanne","last_name":"Dörfler"},{"full_name":"Altheus, Holger","first_name":"Holger","last_name":"Altheus"},{"last_name":"Kaskel","first_name":"Stefan","full_name":"Kaskel, Stefan"},{"full_name":"Prehal, Christian","first_name":"Christian","orcid":"0000-0003-0654-0940","last_name":"Prehal"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander"}],"title":"Current status and future perspectives of lithium metal batteries","article_number":"228803","status":"public","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jpowsour.2020.228803"}],"publisher":"Elsevier","publication":"Journal of Power Sources","intvolume":"       480","issue":"12","date_created":"2020-09-10T10:48:40Z","date_published":"2020-12-31T00:00:00Z","month":"12","volume":480,"article_type":"original","day":"31","citation":{"short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020).","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. <i>Journal of Power Sources</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">https://doi.org/10.1016/j.jpowsour.2020.228803</a>","ieee":"A. Varzi <i>et al.</i>, “Current status and future perspectives of lithium metal batteries,” <i>Journal of Power Sources</i>, vol. 480, no. 12. Elsevier, 2020.","ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803.","ama":"Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. <i>Journal of Power Sources</i>. 2020;480(12). doi:<a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">10.1016/j.jpowsour.2020.228803</a>","mla":"Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” <i>Journal of Power Sources</i>, vol. 480, no. 12, 228803, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">10.1016/j.jpowsour.2020.228803</a>.","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” <i>Journal of Power Sources</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">https://doi.org/10.1016/j.jpowsour.2020.228803</a>."},"date_updated":"2023-08-22T09:20:37Z","related_material":{"record":[{"id":"8067","relation":"earlier_version","status":"public"}]},"publication_identifier":{"issn":["0378-7753"]},"article_processing_charge":"No","acknowledgement":"A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of  Ferrara (Department of  Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at  Dresden and would like to  acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria.","abstract":[{"text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.","lang":"eng"}],"external_id":{"isi":["000593857300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"StFr"}],"language":[{"iso":"eng"}],"_id":"8361","publication_status":"published","oa_version":"Published Version","doi":"10.1016/j.jpowsour.2020.228803","isi":1,"year":"2020","type":"journal_article"},{"year":"2020","type":"dissertation","oa_version":"Published Version","doi":"10.15479/AT:ISTA:8366","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"}],"department":[{"_id":"BeBi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"_id":"8366","language":[{"iso":"eng"}],"publication_status":"published","ddc":["000"],"article_processing_charge":"No","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","alternative_title":["ISTA Thesis"],"file_date_updated":"2020-09-16T15:11:01Z","publication_identifier":{"isbn":["978-3-99078-010-7"],"issn":["2663-337X"]},"ec_funded":1,"abstract":[{"text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop.","lang":"eng"}],"date_updated":"2024-02-21T12:44:29Z","day":"21","citation":{"short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","apa":"Guseinov, R. (2020). <i>Computational design of curved thin shells: From glass façades to programmable matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8366\">https://doi.org/10.15479/AT:ISTA:8366</a>","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8366\">10.15479/AT:ISTA:8366</a>","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","mla":"Guseinov, Ruslan. <i>Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8366\">10.15479/AT:ISTA:8366</a>.","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8366\">https://doi.org/10.15479/AT:ISTA:8366</a>."},"file":[{"date_updated":"2020-09-10T16:11:49Z","success":1,"file_name":"thesis_rguseinov.pdf","checksum":"f8da89553da36037296b0a80f14ebf50","creator":"rguseino","file_id":"8367","relation":"main_file","file_size":70950442,"date_created":"2020-09-10T16:11:49Z","content_type":"application/pdf","access_level":"open_access"},{"creator":"rguseino","file_id":"8374","relation":"source_file","file_size":76207597,"date_created":"2020-09-11T09:39:48Z","content_type":"application/x-zip-compressed","access_level":"closed","date_updated":"2020-09-16T15:11:01Z","file_name":"thesis_source.zip","checksum":"e8fd944c960c20e0e27e6548af69121d"}],"related_material":{"record":[{"status":"deleted","id":"7151","relation":"research_data"},{"relation":"part_of_dissertation","id":"7262","status":"public"},{"id":"8562","relation":"part_of_dissertation","status":"public"},{"id":"1001","relation":"part_of_dissertation","status":"public"},{"relation":"research_data","id":"8375","status":"public"}]},"month":"09","date_created":"2020-09-10T16:19:55Z","date_published":"2020-09-21T00:00:00Z","degree_awarded":"PhD","has_accepted_license":"1","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"page":"118","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"author":[{"full_name":"Guseinov, Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","orcid":"0000-0001-9819-5077","first_name":"Ruslan"}],"oa":1,"status":"public","title":"Computational design of curved thin shells: From glass façades to programmable matter"},{"publisher":"Institute of Science and Technology Austria","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"BeBi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"_id":"8375","oa":1,"file_date_updated":"2020-09-11T09:52:36Z","author":[{"full_name":"Guseinov, Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","orcid":"0000-0001-9819-5077","last_name":"Guseinov"}],"article_processing_charge":"No","contributor":[{"orcid":"0000-0001-9819-5077","last_name":"Guseinov","first_name":"Ruslan","contributor_type":"researcher","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Connor","last_name":"McMahan","contributor_type":"researcher"},{"last_name":"Perez Rodriguez","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Daraio","first_name":"Chiara"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd","contributor_type":"researcher","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape."}],"title":"Supplementary data for \"Computational design of curved thin shells: from glass façades to programmable matter\"","status":"public","ec_funded":1,"file":[{"file_id":"8376","creator":"rguseino","relation":"main_file","file_size":29214988,"date_created":"2020-09-11T09:45:21Z","content_type":"video/mp4","access_level":"open_access","date_updated":"2020-09-11T09:45:21Z","file_name":"supplementary_movie_1.mp4","success":1,"checksum":"4029ffd65fb82ef2366b2fc2a4908e16"},{"date_created":"2020-09-11T09:45:25Z","file_size":28449475,"file_id":"8377","relation":"main_file","creator":"rguseino","access_level":"open_access","content_type":"video/mp4","success":1,"file_name":"supplementary_movie_2.mp4","date_updated":"2020-09-11T09:45:25Z","checksum":"8ed03b04d80f1a4e622cb22e6100afd8"},{"checksum":"ad6864afb5e694e5c52a88fba4e02eea","success":1,"file_name":"supplementary_movie_3.mp4","date_updated":"2020-09-11T09:45:28Z","access_level":"open_access","content_type":"video/mp4","date_created":"2020-09-11T09:45:28Z","file_size":26315853,"relation":"main_file","file_id":"8378","creator":"rguseino"},{"success":1,"file_name":"supplementary_movie_4.mp4","date_updated":"2020-09-11T09:45:33Z","checksum":"b079cef7871fe1afb69af0e2b099f3b1","date_created":"2020-09-11T09:45:33Z","file_size":25198755,"file_id":"8379","relation":"main_file","creator":"rguseino","access_level":"open_access","content_type":"video/mp4"},{"checksum":"9d1d48a8ed5c109a999c51b044ee523d","date_updated":"2020-09-11T09:45:36Z","success":1,"file_name":"supplementary_movie_5.mp4","content_type":"video/mp4","access_level":"open_access","relation":"main_file","creator":"rguseino","file_id":"8380","file_size":29011354,"date_created":"2020-09-11T09:45:36Z"},{"date_updated":"2020-09-11T09:52:36Z","success":1,"file_name":"readme.txt","checksum":"d414d0059e982d752d218756b3c3ce05","file_size":586,"file_id":"8381","creator":"rguseino","relation":"main_file","date_created":"2020-09-11T09:52:36Z","content_type":"text/plain","access_level":"open_access"}],"day":"21","citation":{"ieee":"R. Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.","short":"R. Guseinov, (2020).","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8375\">https://doi.org/10.15479/AT:ISTA:8375</a>","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8375\">https://doi.org/10.15479/AT:ISTA:8375</a>.","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8375\">10.15479/AT:ISTA:8375</a>.","ama":"Guseinov R. Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8375\">10.15479/AT:ISTA:8375</a>","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8375\">10.15479/AT:ISTA:8375</a>."},"date_updated":"2024-02-21T12:44:29Z","type":"research_data","year":"2020","related_material":{"record":[{"status":"public","id":"8366","relation":"used_in_publication"}]},"oa_version":"Published Version","date_created":"2020-09-11T09:52:54Z","date_published":"2020-09-21T00:00:00Z","month":"09","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","doi":"10.15479/AT:ISTA:8375"},{"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"first_name":"Faith","last_name":"Ellen","full_name":"Ellen, Faith"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"full_name":"Zhu, Leqi","last_name":"Zhu","first_name":"Leqi"}],"article_processing_charge":"No","publication_identifier":{"isbn":["9781450375825"]},"status":"public","abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We explain why this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.","lang":"eng"}],"title":"Brief Announcement: Why Extension-Based Proofs Fail","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","publisher":"Association for Computing Machinery","quality_controlled":"1","page":"54-56","publication_status":"published","language":[{"iso":"eng"}],"_id":"8383","month":"07","oa_version":"None","date_created":"2020-09-13T22:01:18Z","date_published":"2020-07-31T00:00:00Z","doi":"10.1145/3382734.3405743","date_updated":"2024-02-28T12:54:19Z","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Brief Announcement: Why Extension-Based Proofs Fail.” In <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, 54–56. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3382734.3405743\">https://doi.org/10.1145/3382734.3405743</a>.","mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Why Extension-Based Proofs Fail.” <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2020, pp. 54–56, doi:<a href=\"https://doi.org/10.1145/3382734.3405743\">10.1145/3382734.3405743</a>.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Brief Announcement: Why Extension-Based Proofs Fail. In: <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2020:54-56. doi:<a href=\"https://doi.org/10.1145/3382734.3405743\">10.1145/3382734.3405743</a>","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2020. Brief Announcement: Why Extension-Based Proofs Fail. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 54–56.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Brief Announcement: Why Extension-Based Proofs Fail,” in <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2020, pp. 54–56.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2020). Brief Announcement: Why Extension-Based Proofs Fail. In <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i> (pp. 54–56). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3382734.3405743\">https://doi.org/10.1145/3382734.3405743</a>"},"day":"31","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2020-08-07","start_date":"2020-08-03","location":"Virtual, Italy"},"scopus_import":"1","type":"conference","year":"2020"},{"external_id":{"isi":["000583700300004"]},"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"ChWo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","ddc":["000"],"language":[{"iso":"eng"}],"_id":"8384","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"file_date_updated":"2020-11-23T09:03:19Z","article_processing_charge":"No","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","abstract":[{"text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.","lang":"eng"}],"ec_funded":1,"scopus_import":"1","type":"journal_article","year":"2020","isi":1,"oa_version":"Submitted Version","doi":"10.1145/3386569.3392405","publisher":"Association for Computing Machinery","main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392405","open_access":"1"}],"quality_controlled":"1","intvolume":"        39","publication":"ACM Transactions on Graphics","issue":"4","acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"author":[{"full_name":"Ishida, Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige","last_name":"Ishida"},{"first_name":"Peter","last_name":"Synak","full_name":"Synak, Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narita","first_name":"Fumiya","full_name":"Narita, Fumiya"},{"first_name":"Toshiya","last_name":"Hachisuka","full_name":"Hachisuka, Toshiya"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"article_number":"31","title":"A model for soap film dynamics with evolving thickness","status":"public","file":[{"checksum":"813831ca91319d794d9748c276b24578","file_name":"2020_soapfilm_submitted.pdf","success":1,"date_updated":"2020-11-23T09:03:19Z","access_level":"open_access","content_type":"application/pdf","date_created":"2020-11-23T09:03:19Z","creator":"dernst","file_id":"8795","relation":"main_file","file_size":14935529}],"day":"08","citation":{"short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., &#38; Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>.","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>."},"date_updated":"2024-02-28T12:57:31Z","date_created":"2020-09-13T22:01:18Z","date_published":"2020-07-08T00:00:00Z","month":"07","has_accepted_license":"1","article_type":"original","volume":39},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChWo"}],"external_id":{"isi":["000583700300021"]},"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176"}],"publication_status":"published","ddc":["000"],"_id":"8385","language":[{"iso":"eng"}],"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","article_processing_charge":"No","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"file_date_updated":"2020-11-23T09:01:22Z","ec_funded":1,"abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"scopus_import":"1","type":"journal_article","isi":1,"year":"2020","oa_version":"Submitted Version","doi":"10.1145/3386569.3392412","intvolume":"        39","publication":"ACM Transactions on Graphics","publisher":"Association for Computing Machinery","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392412"}],"quality_controlled":"1","issue":"4","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"last_name":"Sperl","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg"},{"last_name":"Narain","first_name":"Rahul","full_name":"Narain, Rahul"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"status":"public","article_number":"48","title":"Homogenized yarn-level cloth","date_updated":"2024-02-28T12:57:47Z","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":38922662,"file_id":"8794","relation":"main_file","creator":"dernst","date_created":"2020-11-23T09:01:22Z","checksum":"cf4c1d361c3196c4bd424520a5588205","date_updated":"2020-11-23T09:01:22Z","success":1,"file_name":"2020_hylc_submitted.pdf"}],"day":"08","citation":{"ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392412\">10.1145/3386569.3392412</a>","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392412\">10.1145/3386569.3392412</a>.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392412\">https://doi.org/10.1145/3386569.3392412</a>.","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2020). Homogenized yarn-level cloth. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392412\">https://doi.org/10.1145/3386569.3392412</a>","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020."},"related_material":{"record":[{"relation":"dissertation_contains","id":"12358","status":"public"}]},"month":"07","date_created":"2020-09-13T22:01:18Z","date_published":"2020-07-08T00:00:00Z","article_type":"original","volume":39,"has_accepted_license":"1"},{"publication_status":"published","ddc":["003"],"language":[{"iso":"eng"}],"_id":"8386","department":[{"_id":"BeBi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"ec_funded":1,"abstract":[{"text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2020-09-15T12:51:53Z","type":"dissertation","year":"2020","doi":"10.15479/AT:ISTA:8386","supervisor":[{"first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"publisher":"Institute of Science and Technology Austria","page":"148","status":"public","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","author":[{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Ran","first_name":"Ran","last_name":"Zhang","orcid":"0000-0002-3808-281X"}],"oa":1,"related_material":{"record":[{"id":"486","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1002"}]},"date_updated":"2023-09-22T09:49:31Z","file":[{"date_created":"2020-09-14T01:02:59Z","file_id":"8388","relation":"source_file","creator":"rzhang","file_size":1245800191,"access_level":"closed","content_type":"application/x-zip-compressed","file_name":"Thesis_Ran.zip","date_updated":"2020-09-14T12:18:43Z","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba"},{"checksum":"817e20c33be9247f906925517c56a40d","date_updated":"2020-09-15T12:51:53Z","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"rzhang","file_id":"8396","file_size":161385316,"date_created":"2020-09-15T12:51:53Z"}],"day":"14","citation":{"ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8386\">10.15479/AT:ISTA:8386</a>","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","mla":"Zhang, Ran. <i>Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8386\">10.15479/AT:ISTA:8386</a>.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8386\">https://doi.org/10.15479/AT:ISTA:8386</a>.","apa":"Zhang, R. (2020). <i>Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8386\">https://doi.org/10.15479/AT:ISTA:8386</a>","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020."},"degree_awarded":"PhD","has_accepted_license":"1","month":"09","date_published":"2020-09-14T00:00:00Z","date_created":"2020-09-14T01:04:53Z"},{"article_processing_charge":"No","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"file_date_updated":"2020-09-14T13:39:17Z","abstract":[{"text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ChLa"}],"publication_status":"published","ddc":["000"],"_id":"8390","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:8390","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"}],"year":"2020","type":"dissertation","author":[{"first_name":"Amélie","last_name":"Royer","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","full_name":"Royer, Amélie"}],"oa":1,"status":"public","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","publisher":"Institute of Science and Technology Austria","page":"197","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"month":"09","date_published":"2020-09-14T00:00:00Z","date_created":"2020-09-14T13:42:09Z","degree_awarded":"PhD","has_accepted_license":"1","date_updated":"2023-10-16T10:04:02Z","file":[{"checksum":"c914d2f88846032f3d8507734861b6ee","date_updated":"2020-09-14T13:39:14Z","success":1,"file_name":"2020_Thesis_Royer.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"8391","creator":"dernst","relation":"main_file","file_size":30224591,"date_created":"2020-09-14T13:39:14Z"},{"checksum":"ae98fb35d912cff84a89035ae5794d3c","file_name":"thesis_sources.zip","date_updated":"2020-09-14T13:39:17Z","access_level":"closed","content_type":"application/x-zip-compressed","date_created":"2020-09-14T13:39:17Z","file_size":74227627,"file_id":"8392","relation":"main_file","creator":"dernst"}],"citation":{"chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","mla":"Royer, Amélie. <i>Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>.","apa":"Royer, A. (2020). <i>Leveraging structure in Computer Vision tasks for flexible Deep Learning models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020."},"day":"14","related_material":{"record":[{"relation":"part_of_dissertation","id":"7936","status":"public"},{"status":"public","id":"7937","relation":"part_of_dissertation"},{"id":"8193","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8092","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"911"}]}},{"has_accepted_license":"1","volume":133,"article_type":"original","date_created":"2020-09-17T14:00:33Z","date_published":"2020-04-09T00:00:00Z","month":"04","citation":{"apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","ieee":"G. A. Dimchev <i>et al.</i>, “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” <i>Journal of Cell Science</i>, vol. 133, no. 7. The Company of Biologists, 2020.","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. 2020;133(7). doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>."},"day":"09","file":[{"file_name":"2020_JournalCellScience_Dimchev.pdf","date_updated":"2020-10-11T22:30:02Z","embargo":"2020-10-10","checksum":"ba917e551acc4ece2884b751434df9ae","date_created":"2020-09-17T14:07:51Z","file_size":13493302,"creator":"dernst","relation":"main_file","file_id":"8435","access_level":"open_access","content_type":"application/pdf"}],"date_updated":"2023-09-05T15:41:48Z","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","article_number":"jcs239020","status":"public","oa":1,"author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"full_name":"Humphries, Ashley C.","first_name":"Ashley C.","last_name":"Humphries"},{"first_name":"Matthias","last_name":"Schaks","full_name":"Schaks, Matthias"},{"full_name":"Dimchev, Vanessa","last_name":"Dimchev","first_name":"Vanessa"},{"last_name":"Stradal","first_name":"Theresia E. B.","full_name":"Stradal, Theresia E. B."},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"full_name":"Krause, Matthias","last_name":"Krause","first_name":"Matthias"},{"full_name":"Way, Michael","first_name":"Michael","last_name":"Way"},{"first_name":"Martin","last_name":"Falcke","full_name":"Falcke, Martin"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"}],"issue":"7","keyword":["Cell Biology"],"quality_controlled":"1","publisher":"The Company of Biologists","publication":"Journal of Cell Science","intvolume":"       133","doi":"10.1242/jcs.239020","oa_version":"Published Version","pmid":1,"isi":1,"year":"2020","type":"journal_article","abstract":[{"text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ","lang":"eng"}],"file_date_updated":"2020-10-11T22:30:02Z","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"article_processing_charge":"No","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","language":[{"iso":"eng"}],"_id":"8434","publication_status":"published","ddc":["570"],"project":[{"call_identifier":"FWF","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales"}],"external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"department":[{"_id":"FlSc"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"intvolume":"        11","publication":"Nature Communications","publisher":"Springer Nature","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"NanoFab"}],"author":[{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold"},{"full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Wulf","orcid":"0000-0001-6613-1378"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","first_name":"Shabir"},{"last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860"},{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Hease","orcid":"0000-0001-9868-2166"},{"orcid":"0000-0001-6937-5773","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"oa":1,"status":"public","article_number":"4460","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","date_updated":"2024-08-07T07:11:51Z","file":[{"checksum":"88f92544889eb18bb38e25629a422a86","file_name":"2020_NatureComm_Arnold.pdf","success":1,"date_updated":"2020-09-18T13:02:37Z","access_level":"open_access","content_type":"application/pdf","date_created":"2020-09-18T13:02:37Z","relation":"main_file","file_id":"8530","creator":"dernst","file_size":1002818}],"day":"08","citation":{"short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>."},"related_material":{"record":[{"status":"public","id":"13056","relation":"research_data"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-18912-9"},{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/"}]},"month":"09","date_created":"2020-09-18T10:56:20Z","date_published":"2020-09-08T00:00:00Z","article_type":"original","volume":11,"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoFi"}],"external_id":{"isi":["000577280200001"]},"project":[{"call_identifier":"H2020","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"publication_status":"published","ddc":["530"],"language":[{"iso":"eng"}],"_id":"8529","article_processing_charge":"No","acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","publication_identifier":{"issn":["2041-1723"]},"file_date_updated":"2020-09-18T13:02:37Z","ec_funded":1,"abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"isi":1,"year":"2020","type":"journal_article","oa_version":"Published Version","doi":"10.1038/s41467-020-18269-z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"quality_controlled":"1","publisher":"MDPI","publication":"International Journal of Molecular Sciences","intvolume":"        21","issue":"18","oa":1,"author":[{"last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep","first_name":"Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481"},{"first_name":"Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","article_number":"6737","status":"public","day":"14","citation":{"ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18. MDPI, 2020.","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., &#38; Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>","mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18, 6737, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. 2020;21(18). doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>."},"file":[{"date_created":"2020-09-21T14:08:58Z","relation":"main_file","creator":"dernst","file_id":"8551","file_size":5748456,"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2020_JournMolecSciences_Kleindienst.pdf","date_updated":"2020-09-21T14:08:58Z","checksum":"2e4f62f3cfe945b7391fc3070e5a289f"}],"date_updated":"2024-03-25T23:30:16Z","related_material":{"record":[{"relation":"dissertation_contains","id":"9562","status":"public"}]},"date_published":"2020-09-14T00:00:00Z","date_created":"2020-09-20T22:01:35Z","month":"09","has_accepted_license":"1","volume":21,"article_type":"original","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020"},{"name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus","_id":"25D32BC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"785907","_id":"26436750-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)"}],"external_id":{"isi":["000579945300001"]},"department":[{"_id":"RySh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8532","language":[{"iso":"eng"}],"publication_status":"published","ddc":["570"],"file_date_updated":"2020-09-21T14:08:58Z","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"article_processing_charge":"No","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","abstract":[{"lang":"eng","text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography."}],"ec_funded":1,"isi":1,"type":"journal_article","year":"2020","scopus_import":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3390/ijms21186737"},{"conference":{"name":"MFCS: Symposium on Mathematical Foundations of Computer Science","location":"Prague, Czech Republic","start_date":"2020-08-24","end_date":"2020-08-28"},"day":"18","citation":{"ieee":"K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Simplified game of life: Algorithms and complexity,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170.","apa":"Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., &#38; Svoboda, J. (2020). Simplified game of life: Algorithms and complexity. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>","short":"K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub Svoboda. “Simplified Game of Life: Algorithms and Complexity.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>.","mla":"Chatterjee, Krishnendu, et al. “Simplified Game of Life: Algorithms and Complexity.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 22:1-22:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Simplified game of life: Algorithms and complexity. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>","ista":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2020. Simplified game of life: Algorithms and complexity. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 22:1-22:13."},"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2020-09-21T13:57:34Z","creator":"dernst","file_id":"8550","relation":"main_file","file_size":491374,"checksum":"bbd7c4f55d45f2ff2a0a4ef0e10a77b1","file_name":"2020_LIPIcs_Chatterjee.pdf","success":1,"date_updated":"2020-09-21T13:57:34Z"}],"date_updated":"2025-06-02T08:53:42Z","has_accepted_license":"1","volume":170,"date_created":"2020-09-20T22:01:36Z","date_published":"2020-08-18T00:00:00Z","month":"08","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"45th International Symposium on Mathematical Foundations of Computer Science","intvolume":"       170","title":"Simplified game of life: Algorithms and complexity","article_number":"22:1-22:13","status":"public","oa":1,"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jecker","first_name":"Ismael R","full_name":"Jecker, Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425"},{"first_name":"Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"}],"arxiv":1,"type":"conference","year":"2020","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"doi":"10.4230/LIPIcs.MFCS.2020.22","oa_version":"Published Version","_id":"8533","language":[{"iso":"eng"}],"ddc":["000"],"publication_status":"published","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"arxiv":["2007.02894"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete."}],"ec_funded":1,"file_date_updated":"2020-09-21T13:57:34Z","publication_identifier":{"isbn":["9783959771597"],"issn":["18688969"]},"alternative_title":["LIPIcs"],"article_processing_charge":"No","acknowledgement":"Krishnendu Chatterjee: The research was partially supported by the Vienna Science and\r\nTechnology Fund (WWTF) Project ICT15-003.\r\nIsmaël Jecker: This project has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411."},{"scopus_import":"1","type":"conference","year":"2020","doi":"10.4230/LIPIcs.MFCS.2020.51","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"oa_version":"Published Version","publication_status":"published","ddc":["000"],"language":[{"iso":"eng"}],"_id":"8534","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"ec_funded":1,"abstract":[{"text":"A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs.","lang":"eng"}],"acknowledgement":"Ismaël Jecker: This project has received funding from the European Union’s Horizon\r\n2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.\r\n754411. Nicolas Mazzocchi: PhD fellowship FRIA from the F.R.S.-FNRS.","article_processing_charge":"No","alternative_title":["LIPIcs"],"publication_identifier":{"isbn":["9783959771597"],"issn":["18688969"]},"file_date_updated":"2020-09-21T14:17:08Z","conference":{"name":"MFCS: Symposium on Mathematical Foundations of Computer Science","end_date":"2020-08-28","start_date":"2020-08-24","location":"Prague, Czech Republic"},"date_updated":"2021-01-12T08:19:56Z","file":[{"date_created":"2020-09-21T14:17:08Z","creator":"dernst","relation":"main_file","file_id":"8552","file_size":597977,"access_level":"open_access","content_type":"application/pdf","file_name":"2020_LIPIcsMFCS_Jecker.pdf","success":1,"date_updated":"2020-09-21T14:17:08Z","checksum":"2dc9e2fad6becd4563aef3e27a473f70"}],"citation":{"ama":"Jecker IR, Kupferman O, Mazzocchi N. Unary prime languages. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>","ista":"Jecker IR, Kupferman O, Mazzocchi N. 2020. Unary prime languages. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 51:1-51:12.","mla":"Jecker, Ismael R., et al. “Unary Prime Languages.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 51:1-51:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>.","chicago":"Jecker, Ismael R, Orna Kupferman, and Nicolas Mazzocchi. “Unary Prime Languages.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>.","apa":"Jecker, I. R., Kupferman, O., &#38; Mazzocchi, N. (2020). Unary prime languages. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>","short":"I.R. Jecker, O. Kupferman, N. Mazzocchi, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"I. R. Jecker, O. Kupferman, and N. Mazzocchi, “Unary prime languages,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170."},"day":"18","volume":170,"has_accepted_license":"1","month":"08","date_published":"2020-08-18T00:00:00Z","date_created":"2020-09-20T22:01:36Z","intvolume":"       170","publication":"45th International Symposium on Mathematical Foundations of Computer Science","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","status":"public","article_number":"51:1-51:12","title":"Unary prime languages","author":[{"first_name":"Ismael R","last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"},{"first_name":"Nicolas","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas"}],"oa":1}]